Genes2FANs: Connecting genes through functional association networks

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Dannenfelser, Ruth ^a   Clark, Neil R ^a   Ma'ayan, Avi ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CO-EXPRESSION; COMPLEX DISEASE; DISEASE GENES; FUNCTIONAL ASSOCIATION NETWORKS; FUNCTIONAL ASSOCIATIONS; FUNCTIONAL INTERACTION; GENE LISTS; INTERACTION NETWORKS; INVERSE CORRELATION; MAMMALIAN GENES; ORTHOLOGS; PROTEIN-PROTEIN INTERACTION NETWORKS; SEARCH TERMS; SUB-NETWORK; SUBNETWORKS; TYPE-2 DIABETES; VARIOUS FUNCTIONS; WEB-BASED TOOLS;

ASSOCIATION REACTIONS; DISEASES; MAMMALS; PROTEINS; QUERY PROCESSING;

GENE EXPRESSION;

MAMMALIA;

ANIMAL; ARTICLE; COMPUTER PROGRAM; DISEASES; GENE; GENE REGULATORY NETWORK; GENETICS; HUMAN; INTERNET; MEDLINE; MOUSE; PROTEIN ANALYSIS;

ANIMALS; DISEASE; GENE REGULATORY NETWORKS; GENES; HUMANS; INTERNET; MICE; PROTEIN INTERACTION MAPPING; PUBMED; SOFTWARE;

EID: 84863097993     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-156     Document Type: Article

References (52)

1. Berger SI, Posner JM, Ma'ayan A. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinforma 2007, 8:372.
2. Hu ZJ, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, DeLisi C. VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res 2009, 37:W115-W121. 10.1093/nar/gkp406, 2703932, 19465394.
3. Kamburov A, Pentchev K, Galicka H, Wierling C, Lehrach H, Herwig R. ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res 2011, 39:D712-D717. 10.1093/nar/gkq1156, 3013724, 21071422.
4. Dogrusoz U, Erson EZ, Giral E, Demir E, Babur O, Cetintas A, Colak R. PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinformatics 2006, 22(3):374-375. 10.1093/bioinformatics/bti776, 16287939.
5. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 2011, 39(Database issue):D561-D568. 3013807, 21045058.
6. Kao HL, Gunsalus KC. Browsing multidimensional molecular networks with the generic network browser (N-Browse). Curr Protoc Bioinformatics 2008, Chapter 9:Unit 9-Unit 11.
7. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 2010, 38(Web Server issue):W214-W220. 2896186, 20576703.
8. McDowall MD, Scott MS, Barton GJ. PIPs: human protein-protein interaction prediction database. Nucleic Acids Res 2009, 37(Database issue):D651-D656. 2686497, 18988626.
9. Huttenhower C, Haley EM, Hibbs MA, Dumeaux V, Barrett DR, Coller HA, Troyanskaya OG. Exploring the human genome with functional maps. Genome Res 2009, 19(6):1093-1106. 10.1101/gr.082214.108, 2694471, 19246570.
10. Alexeyenko A, Schmitt T, Tjarnberg A, Guala D, Frings O, Sonnhammer EL. Comparative interactomics with Funcoup 2.0. Nucleic Acids Res 2012, 40(Database issue):D821-D828. 3245127, 22110034.
11. Sharan R, Ulitsky I, Shamir R. Network-based prediction of protein function. Mol Syst Biol 2007, 3:88. 1847944, 17353930.
12. Jiang T, Keating AE. AVID: an integrative framework for discovering functional relationships among proteins. BMC Bioinforma 2005, 6:136.
13. Yu H, Paccanaro A, Trifonov V, Gerstein M. Predicting interactions in protein networks by completing defective cliques. Bioinformatics 2006, 22(7):823-829. 10.1093/bioinformatics/btl014, 16455753.
14. Cordeddu V, Di Schiavi E, Pennacchio LA. Ma'ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, Martin J, Schackwitz W, et al: Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet 2009, 41(9):1022-1026. 10.1038/ng.425, 2765465, 19684605.
15. Bromberg KD. Ma'ayan A, Neves SR, Iyengar R: Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science 2008, 320(5878):903-909. 10.1126/science.1152662, 2776723, 18487186.
16. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
17. Myers CL, Robson D, Wible A, Hibbs MA, Chiriac C, Theesfeld CL, Dolinski K, Troyanskaya OG. Discovery of biological networks from diverse functional genomic data. Genome Biol 2005, 6(13).
18. Berger SI, Iyengar R, Ma'ayan A. AVIS: AJAX viewer of interactive signaling networks. Bioinformatics 2007, 23(20):2803-2805. 10.1093/bioinformatics/btm444, 2724864, 17855420.
19. Dannenfelser R, Lachmann A, Szenk M, Ma'ayan A. FNV: light-weight flash-based network and pathway viewer. Bioinformatics 2011, 27(8):1181-1182. 10.1093/bioinformatics/btr098, 3072557, 21349871.
20. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Cytoscape Web: an interactive web-based network browser. Bioinformatics 2010, 26(18):2347-2348. 10.1093/bioinformatics/btq430, 2935447, 20656902.
21. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, Lerner J, Brunet JP, Subramanian A, Ross KN, et al. The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease. Science 2006, 313(5795):1929-1935. 10.1126/science.1132939, 17008526.
22. Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma'ayan A. ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 2010, 26(19):2438-2444. 10.1093/bioinformatics/btq466, 2944209, 20709693.
23. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res 2006, 34(Database issue):D108-110. 1347505, 16381825.
24. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
25. Culhane AC, Schwarzl T, Sultana R, Picard KC, Picard SC, Lu TH, Franklin KR, French SJ, Papenhausen G, Correll M, et al. GeneSigDB-a curated database of gene expression signatures. Nucleic Acids Res 2010, 38:D716-D725. 10.1093/nar/gkp1015, 2808880, 19934259.
26. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120(1):15-20. 10.1016/j.cell.2004.12.035, 15652477.
27. Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE. The Mouse Genome Database genotypes::phenotypes. Nucleic Acids Res 2009, 37(Database issue):D712-719. 2686566, 18981050.
28. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, et al. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 2009, 37:D603-D610. 10.1093/nar/gkn810, 2686599, 18953024.
29. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, et al. The Pfam protein families database. Nucleic Acids Res 2010, 38:D211-D222. 10.1093/nar/gkp985, 2808889, 19920124.
30. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. InterPro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-D215. 10.1093/nar/gkn785, 2686546, 18940856.
31. Hamosh A, Scott AF, Amberger J, Bocchini C, Valle D, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2002, 30(1):52-55. 10.1093/nar/30.1.52, 99152, 11752252.
32. Lachmann A, Ma'ayan A. Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinforma 2010, 11:87.
33. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, et al. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res 2011, 39(Database issue):D1035-1041. 3013709, 21059682.
34. Ceol A, Aryamontri AC, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2010, 38:D532-D539. 10.1093/nar/gkp983, 2808973, 19897547.
35. Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan THW, Shah N, et al. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 2008, 4: . 2615304, 19096361.
36. Prasad TSK, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al. Human Protein Reference Database-2009 update. Nucleic Acids Res 2009, 37:D767-D772. 10.1093/nar/gkn892, 2686490, 18988627.
37. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-D360. 10.1093/nar/gkp896, 2808910, 19880382.
38. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res 2010, 38:D525-D531. 10.1093/nar/gkp878, 2808934, 19850723.
39. Stark C, Breitkreutz BJ, Chatr-aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang XD, Shi XQ, et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 2011, 39:D698-D704. 10.1093/nar/gkq1116, 3013707, 21071413.
40. Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, et al. The HUPO PSI's molecular interaction format-a community standard for the representation of protein interaction data. Nat Biotechnol 2004, 22(2):177-183. 10.1038/nbt926, 14755292.
41. Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, et al. The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res 2005, 33:D418-D424. 540005, 15608229.
42. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004, 32:D449-D451. 10.1093/nar/gkh086, 308820, 14681454.
43. Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, Dubin-Thalere B, Eungdamrong NJ, Weng GZ, Ram PT, Rice JJ, et al. Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science 2005, 309(5737):1078-1083. 10.1126/science.1108876, 3032439, 16099987.
44. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, et al. A human protein-protein interaction network: A resource for annotating the proteome. Cell 2005, 122(6):957-968. 10.1016/j.cell.2005.08.029, 16169070.
45. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437(7062):1173-1178. 10.1038/nature04209, 16189514.
46. Yu JY, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 2007, 318(5858):1917-1920. 10.1126/science.1151526, 18029452.
47. Patil A, Nakamura H. Filtering high-throughput protein-protein interaction data using a combination of genomic features. BMC Bioinforma 2005, 6:100.
48. Chen J, Aronow BJ, Jegga AG. Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinforma 2009, 10:73.
49. Navlakha S, Kingsford C. The power of protein interaction networks for associating genes with diseases. Bioinformatics 2010, 26(8):1057-1063. 10.1093/bioinformatics/btq076, 2853684, 20185403.
50. Oti M, Snel B, Huynen MA, Brunner HG. Predicting disease genes using protein-protein interactions. J Med Genet 2006, 43(8):691-698. 10.1136/jmg.2006.041376, 2564594, 16611749.
51. Zhang W, Sun F, Jiang R. Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. BMC Bioinforma 2011, 12(Suppl 1):S11.
52. Kann MG. Advances in translational bioinformatics: computational approaches for the hunting of disease genes. Brief Bioinform 11(1):96-110.